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- PDB-1sz6: MISTLETOE LECTIN I FROM VISCUM ALBUM. CRYSTAL STRUCTURE AT 2.05 A... -

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Basic information

Entry
Database: PDB / ID: 1sz6
TitleMISTLETOE LECTIN I FROM VISCUM ALBUM. CRYSTAL STRUCTURE AT 2.05 A RESOLUTION
Components
  • BETA-GALACTOSIDE SPECIFIC LECTIN I B CHAIN
  • RRNA N-GLYCOSIDASE A CHAIN
KeywordsHYDROLASE INHIBITOR / RIBOSOME-INACTIVATING PROTEIN TYPE II
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / carbohydrate binding / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / Beta-galactoside-specific lectin 1
Similarity search - Component
Biological speciesViscum album (European mistletoe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGabdoulkhakov, A.G. / Guhlistova, N.E. / Lyashenko, A.V. / Krauspenhaar, R. / Stoeva, S. / Voelter, W. / Nikonov, S.V. / Betzel, C. / Mikhailov, A.M.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Viscum album Mistletoe Lectin I in native state at 2.05 A resolution, comparison of structure active site conformation in ricin and in viscumin
Authors: Gabdoulkhakov, A.G. / Guhlistova, N.E. / Lyashenko, A.V. / Krauspenhaar, R. / Stoeva, S. / Voelter, W. / Nikonov, S.V. / Betzel, C. / Mikhailov, A.M.
History
DepositionApr 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.classification / _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The sequence of the protein was not deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RRNA N-GLYCOSIDASE A CHAIN
B: BETA-GALACTOSIDE SPECIFIC LECTIN I B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,25227
Polymers55,6922
Non-polymers2,55925
Water5,729318
1
A: RRNA N-GLYCOSIDASE A CHAIN
B: BETA-GALACTOSIDE SPECIFIC LECTIN I B CHAIN
hetero molecules

A: RRNA N-GLYCOSIDASE A CHAIN
B: BETA-GALACTOSIDE SPECIFIC LECTIN I B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,50354
Polymers111,3854
Non-polymers5,11950
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Unit cell
Length a, b, c (Å)106.880, 106.880, 310.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-3188-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: x, x-y, 5/6-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein RRNA N-GLYCOSIDASE A CHAIN


Mass: 27226.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P81446
#2: Protein BETA-GALACTOSIDE SPECIFIC LECTIN I B CHAIN


Mass: 28465.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P81446

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Sugars , 1 types, 4 molecules

#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 339 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.49 Å3/Da / Density % sol: 72.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2.5
Details: 40% SATURATED AMMONIUM SULPHATE, 30% GLYCEROL IN 0.1M, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8453 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 16, 2001 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8453 Å / Relative weight: 1
ReflectionResolution: 2.05→29 Å / Num. obs: 65558 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.46 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.058 / Net I/σ(I): 19.2
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.82 / Num. unique all: 5993 / Rsym value: 0.229 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2MLL

2mll


Resolution: 2.05→29 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4701342.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3238 5 %RANDOM
Rwork0.211 ---
all0.213 65558 --
obs0.211 64820 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.6243 Å2 / ksol: 0.35406 e/Å3
Displacement parametersBiso mean: 49 Å2
Baniso -1Baniso -2Baniso -3
1-4.93 Å24.02 Å20 Å2
2--4.93 Å20 Å2
3----9.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.05→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 0 162 318 4397
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it2.91.5
X-RAY DIFFRACTIONc_mcangle_it4.552
X-RAY DIFFRACTIONc_scbond_it4.92
X-RAY DIFFRACTIONc_scangle_it6.892.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 507 4.9 %
Rwork0.357 9777 -
obs-9777 94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2AZI.PARAMAZI.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5NAG.PARAMNAG.TOP

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